I hope this runtime can be done this year... module is the way against GDNative, best integration with GDScript. You should no translate bones to nodes because performance, Spine node should be one node and controllable with gdscript, bones, meshes, animations, z-order, etc... should be exposed to scripting sysem and if user need to attach one bone to a position or changing z-order, something like this, they can write exported variables to see that in inspector or make gdscipt logic to change that bone/mesh/texture/whatever in runtime...
We are waiting for this, please don´t forgot, in 2018 Godot it much more used that many of the other API´s that are now soported officially by spine, and behind Unity/Unreal/GameMaker, Godot is becoming the open-source alternative to this aplications.